NCBI RefSeq: reference sequence standards through 25 years of curation and annotation.

Reference sequences and annotations serve as the foundation for many lines of research today, from organism and sequence identification to providing a core description of the genes, transcripts and proteins found in an organism's genome. Interpretation of data including transcriptomics, proteomics, sequence variation and comparative analyses based on reference gene annotations informs our understanding of gene function and possible disease mechanisms, leading to new biomedical discoveries. The Reference Sequence (RefSeq) resource created at the National Center for Biotechnology Information (NCBI) leverages both automatic processes and expert curation to create a robust set of reference sequences of genomic, transcript and protein data spanning the tree of life.

Structure-activity relationship study of small-molecule inhibitor of Atg12-Atg3 protein-protein interaction.

Autophagy is a catabolic process that was described to play a critical role in advanced stages of cancer, wherein it maintains tumor cell homeostasis and growth by supplying nutrients. Autophagy is also described to support alternative cellular trafficking pathways, providing a non-canonical autophagy-dependent inflammatory cytokine secretion mechanism. Therefore, autophagy inhibitors have high potential in the treatment of cancer and acute inflammation.

WIPI2b recruitment to phagophores and ATG16L1 binding are regulated by ULK1 phosphorylation.

One of the key events in autophagy is the formation of a double-membrane phagophore, and many regulatory mechanisms underpinning this remain under investigation. WIPI2b is among the first proteins to be recruited to the phagophore and is essential for stimulating autophagy flux by recruiting the ATG12-ATG5-ATG16L1 complex, driving LC3 and GABARAP lipidation. Here, we set out to investigate how WIPI2b function is regulated by phosphorylation.

Loss of EIF4G2 mediates aggressiveness in distinct human endometrial cancer subpopulations with poor survival outcome in patients.

The non-canonical translation initiation factor EIF4G2 plays essential roles in cellular stress responses via translation of selective mRNA cohorts. Currently there is limited and conflicting information regarding its involvement in cancer development and progression. Here we assessed its role in endometrial cancer (EC), in a cohort of 280 EC patients across different types, grades, and stages, and found that low EIF4G2 expression highly correlated with poor overall- and recurrence-free survival in Grade 2 EC patients, monitored over a period of up to 12 years.

Loss-of-function cancer-linked mutations in the EIF4G2 non-canonical translation initiation factor.

Tumor cells often exploit the protein translation machinery, resulting in enhanced protein expression essential for tumor growth. Since canonical translation initiation is often suppressed because of cell stress in the tumor microenvironment, non-canonical translation initiation mechanisms become particularly important for shaping the tumor proteome. EIF4G2 is a non-canonical translation initiation factor that mediates internal ribosome entry site (IRES)- and uORF-dependent initiation mechanisms, which can be used to modulate protein expression in cancer.

Database resources of the National Center for Biotechnology Information.

The National Center for Biotechnology Information (NCBI) provides online information resources for biology, including the GenBank® nucleic acid sequence database and the PubMed® database of citations and abstracts published in life science journals. NCBI provides search and retrieval operations for most of these data from 35 distinct databases. The E-utilities serve as the programming interface for most of these databases.

Identifying a selective inhibitor of autophagy that targets ATG12-ATG3 protein-protein interaction.

Macroautophagy/autophagy is a catabolic process by which cytosolic content is engulfed, degraded and recycled. It has been implicated as a critical pathway in advanced stages of cancer, as it maintains tumor cell homeostasis and continuous growth by nourishing hypoxic or nutrient-starved tumors. Autophagy also supports alternative cellular trafficking pathways, providing a mechanism of non-canonical secretion of inflammatory cytokines.

Apoptotic cell death in disease-Current understanding of the NCCD 2023.

Apoptosis is a form of regulated cell death (RCD) that involves proteases of the caspase family. Pharmacological and genetic strategies that experimentally inhibit or delay apoptosis in mammalian systems have elucidated the key contribution of this process not only to (post-)embryonic development and adult tissue homeostasis, but also to the etiology of multiple human disorders. Consistent with this notion, while defects in the molecular machinery for apoptotic cell death impair organismal development and promote oncogenesis, the unwarranted activation of apoptosis promotes cell loss and tissue damage in the context of various neurological, cardiovascular, renal, hepatic, infectious, neoplastic and inflammatory conditions.

Collection and curation of prokaryotic genome assemblies from type strains at NCBI.

The public sequence databases are entrusted with the dual responsibility of providing an accessible archive to all submitters and supporting data reliability and its re-use to all users. Genomes from type materials can act as an unambiguous reference for a taxonomic name and play an important role in comparative genomics, especially for taxon verification or reclassification. The National Center for Biotechnology Information (NCBI) collects and curates information on prokaryotic type strains and genomes from type strains.

Comprehensive collection of COVID-19 related prosthetic valve failure: a systematic review.

Since the beginning of the SARS-CoV-2 (COVID-19) pandemic, correlation of venous thromboembolism (VTE) and COVID-19 infection has been well established. Increased inflammatory response in the setting of COVID-19 infection is associated with VTE and hypercoagulability. Venous and arterial thrombotic events in COVID-19 infection have been well documented; however, few cases have been reported involving cardiac valve prostheses.

Postdischarge Noninvasive Telemonitoring and Nurse Telephone Coaching Improve Outcomes in Heart Failure Patients With High Burden of Comorbidity.

Background: Noninvasive telemonitoring and nurse telephone coaching (NTM-NTC) is a promising postdischarge strategy in heart failure (HF). Comorbid conditions and disease burden influence health outcomes in HF, but how comorbidity burden modulates the effectiveness of NTM-NTC is unknown. This study aims to identify patients with HF who may benefit from postdischarge NTM-NTC based on their burden of comorbidity.

DAP5 drives translation of specific mRNA targets with upstream ORFs in human embryonic stem cells.

Death associated protein 5 (DAP5/eIF4G2/NAT1) is a member of the eIF4G translation initiation factors that has been shown to mediate noncanonical and/or cap-independent translation. It is essential for embryonic development and for differentiation of embryonic stem cells (ESCs), specifically its ability to drive translation of specific target mRNAs. In order to expand the repertoire of DAP5 target mRNAs, we compared ribosome profiles in control and DAP5 knockdown (KD) human ESCs (hESCs) to identify mRNAs with decreased ribosomal occupancy upon DAP5 silencing.

A new function for the serine protease HtrA2 in controlling radiation-induced senescence in cancer cells.

Radiation therapy can induce cellular senescence in cancer cells, leading to short-term tumor growth arrest but increased long-term recurrence. To better understand the molecular mechanisms involved, we developed a model of radiation-induced senescence in cultured cancer cells. The irradiated cells exhibited a typical senescent phenotype, including upregulation of p53 and its main target, p21, followed by a sustained reduction in cellular proliferation, changes in cell size and cytoskeleton organization, and senescence-associated beta-galactosidase activity.

Epiblast fragmentation by shedding-a novel mechanism to eliminate cells in post-implantation mouse embryos.

The role of programmed cell death during embryonic development has been described previously, but its specific contribution to peri- and post-implantation stages is still debatable. Here, we used transmission electron microscopy and immunostaining of E5.5-7.

Heterozygous deletions of noncoding parts of the gene cause retinitis pigmentosa via reduced gene expression.

Purpose: Heterozygous mutations in the gene , encoding a pre-mRNA splicing factor, cause autosomal dominant retinitis pigmentosa (adRP) with reduced penetrance. At the molecular level, pathogenicity results from haploinsufficiency, as the largest majority of such mutations trigger nonsense-mediated mRNA decay or involve large deletions of coding exons. We investigated genetically two families with a history of adRP, one of whom showed incomplete penetrance.

Personalized treatments for depressive symptoms in patients with advanced heart failure: A pragmatic randomized controlled trial.

Objectives: Heart Failure is a chronic syndrome affecting over 5.7 million in the US and 26 million adults worldwide with nearly 50% experiencing depressive symptoms. The objective of the study is to compare the effects of two evidence-based treatment options for adult patients with depression and advanced heart failure, on depressive symptom severity, physical and mental health related quality of life (HRQoL), heart-failure specific quality of life, caregiver burden, morbidity, and mortality at 3, 6 and 12-months.

Progressive Visual Loss Without Retinal Detachment in Stickler Syndrome: An Uncommon and Novel Presentation.

Stickler syndrome is known to cause visual handicap due to the high incidence of retinal detachment. We aim to present an unusual case of a child with Stickler syndrome who had progressive visual loss secondary to atrophy of the outer retinal layers not associated with retinal detachment. This is a descriptive case report of a 9-year-old child with ocular history of high myopia who presented to our institution with suboptimal visual acuity in both eyes.

Variable phenotype of Knobloch syndrome due to biallelic mutations in children.

Purpose: Knobloch syndrome is a rare, recessively inherited disorder classically characterized by high myopia, retinal detachment, and occipital encephalocele. Our aim is to report the clinical and genetic findings of four Israeli children affected by Knobloch syndrome.

Methods: Retrospective study of four patients diagnosed with Knobloch syndrome, who underwent full ophthalmic examination, electroretinography, and neuroradiologic imaging.

Venous Thromboembolism in Hospitalized COVID-19 Patients: Systematic Review.

Background: Coagulopathy associated with COVID-19 infection and venous thromboembolism (VTE) have emerged as significant contributors to morbidity among patients infected with SARS-CoV-2.

Objective: We performed a systematic review to estimate VTE incidence in hospitalized patients and to analyze characteristic factors in the VTE cohort.

Methods: We searched PubMed and Google Scholar using specified title search terms "SARS-CoV-2" or "COVID-19" and "venous thromboembolism" and "anticoagulation" among others to identify peer-reviewed journal articles published between June 22, 2019, and June 22, 2020.

Depression in Heart Failure: A Systematic Review.

: This paper sought to identify the instruments used to measure depression in heart failure (HF) and elucidate the impact of treatment interventions on depression in HF. The Preferred Reporting Items for Systematic Reviews and Meta-analyses guidelines were followed. Studies published from 1988 to 2018 covering depression and HF were identified through the review of the PubMed and PsycINFO databases using the keywords: "depres*" AND "heart failure.

The impact of antidepressants on depressive symptom severity, quality of life, morbidity, and mortality in heart failure: a systematic review.

Objective: The purpose of this paper is to review the literature on the impact of antidepressants on depressive symptom severity, quality of life (QoL), morbidity, and mortality in patients with heart failure (HF).

Methods: Following the PRISMA (Preferred Reporting Items for Systematic Reviews and Meta-Analyses) Reporting Items for Systematic Reviews and Meta-Analyses guidelines, studies published from December 1969 to December 2019 that pertain to depression and HF were identified through the use of the PubMed and PsycINFO databases, using the keywords: 'antidepressant*' and 'heart failure.' Two authors independently conducted a focused analysis and reached a final consensus on 17 studies that met the specific selection criteria and passed the study quality checks.

Tumor suppressor death-associated protein kinase 1 inhibits necroptosis by p38 MAPK activation.

Death-associated protein kinase 1 (DAPK1, DAPk, DAPK) is known for its involvement in apoptosis and autophagy-associated cell death. Here, we identified an unexpected function of DAPK1 in suppressing necroptosis. DAPK1-deficiency renders macrophages and dendritic cells susceptible to necroptotic death.

Prognostic value of point-of-care ultrasound during cardiac arrest: a systematic review.

Background: Despite significant improvements in cardiopulmonary resuscitation, sudden cardiac arrest is one of the leading causes of mortality in the United States. Ultrasound is a widely available tool that can be used to evaluate the presence of cardiac wall motion during cardiac arrest. Several clinical studies have evaluated the use of ultrasound to visualize cardiac motion as a predictor of mortality in cardiac arrest patients.